reinit the tree, so we can have metadata

5 files changed, 360 insertions, 0 deletions

diff --git a/sci-chemistry/threeV/Manifest b/sci-chemistry/threeV/Manifest
new file mode 100644
index 000000000000..57d0dc6f4d60
--- /dev/null
+++ b/sci-chemistry/threeV/Manifest
@@ -0,0 +1,7 @@
+AUX threeV-1.2-format-security.patch 7116 SHA256 601a566412b8204048e3846c3c4d7741382b816b25e46b05320040d4e9f515ba SHA512 9ed991640b297090a4b35a8d04f67da4eba21c0cf828a06120fd31a55ca809a3485da8e85db759311c1b136b37ae3214c5c1000cc8fb54491f59f454b22f87d3 WHIRLPOOL 79b7a560885499370010f68f9adf4c1821a81e2fb8ef1c1e489da7e3a97951006964bdb65e73c73b9d40dbcecb3a97d0e7a6277bea68a665bc10165cc09f11bb
+AUX threeV-1.2-gentoo.patch 3085 SHA256 e88ad3a84709b6c948f27cf4e81c0850ba7417cda5c2d7cbc9ff86db6f184db8 SHA512 493fc39b2d3cf1325ea00ad572e8c4c62ae48f55a82fd5eb6a1f7e91900ecfdf6cb174ec43b2fb748d6708099ddb395af34045a4439f1dbc0c574169539344a0 WHIRLPOOL d51af86ea1288fcb1ce07b6f4e282498e1f0a34c02c46677a3a4bb010baa1432aea96823938feaf3643ac383988f0296cac371d587118ca0dcf1d5b1f6d4bc77
+DIST 3v-1.2.tgz 599194 SHA256 ae11ce61e6b7cac6aa07d91914b59507a04a1dbfbe624ed8356154cbabc6e8af SHA512 063747e46be1ab8af585909185b735edbbb760945f9d4d345d478a264e3d90c551d72f578239e7eff7768482d18b34d2b00831f87e109ec87cb36b0fd4e6a757 WHIRLPOOL ca497066f3f48df53432ad6cc358a238e5ed360f40446d977361fd8615ba14562a249c098e6c241924de819b3b27e44c4d69bbdb8abfebc46496cb0f7d3d36a9
+EBUILD threeV-1.2-r1.ebuild 745 SHA256 80e3cb30ea99a5b813e57a4e14c60f6ecf31f741155be5ae3cdd1df4f87f654f SHA512 eec0425c83705264670ccba3d8b839717bf1135114fe7baa637d638fe3214c6bc2ec9e7331b9bfc11e6e1bf530ed6ea73164c400c4344d9ca65b0b244338ee02 WHIRLPOOL dff6a9db7b52a478fe2457718da063be52033ec6caf5627d23a0c028b1df03cfa6b3b35faa94bb0fb24db3246d64174103537eb4abb80aa11a129f9b7854c12c
+MISC ChangeLog 2590 SHA256 08eb2a41838f96a8b65db863d647856de5bf4a861986d95257fd4305ac6b0bf4 SHA512 0a529c12e18e8bf0a26243de29f6a570d2c2c67839b7d59bdfa0ca07f78fbb4b38fa5eee22471221c861dd067fc9d39c2baa84fbb46fe7e02e89f12014c0af83 WHIRLPOOL 4cabaaa4adecc16b0838e93c6c90f17452f5810d9ca5c7fea546b8b05af61404c97aba9cc651fe91131e6cdd28ababdfa55065305f11c7472d6361c28efec658
+MISC ChangeLog-2015 461 SHA256 e8749e891c116adbd3fe69cc7afc4ec906605880b446b2407e0c803606c13cb7 SHA512 7328092b693879e324b62ffc0412275efdcd7ecbff1fdc81d7d9590697261ce56e3e4034ae73e108c8f0de76e905f8a1f46c92ca1162679632a72d651ef8290c WHIRLPOOL 3a2097b716be35f1b7a96336a47357c1d6d8196a25904b8bb4a93f85e55b1c1a5909d6c4307ca4adecba0c9a5dc641b65fce55fecc7af5fd801516d87396f966
+MISC metadata.xml 265 SHA256 88fc04c2e3102afd870cfa235e90f0a80b4ebbb032780d7501ff6c6b654c96a2 SHA512 470f6c178e88c4e83afa46d5e901a45fc2427a779ae832df7fa2d6e25e9e8b4ce77cd3a8fe191e6242d6df3b673f0de6b4f90f1e147aa8b8dd566f18163cc73a WHIRLPOOL ba08ab5455155b3c0c24ed2ec94129b3538b4be93069560166150ee59c57bb197c7b513c5a934e47c138aaf9bd34a4a3a8b63c815e34e2a5435af8056a09961d
diff --git a/sci-chemistry/threeV/files/threeV-1.2-format-security.patch b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
new file mode 100644
index 000000000000..b693559900ad
--- /dev/null
+++ b/sci-chemistry/threeV/files/threeV-1.2-format-security.patch
@@ -0,0 +1,198 @@
+ cavities.cpp |  8 ++++----
+ channel.cpp  | 10 +++++-----
+ fsv_calc.cpp |  8 ++++----
+ solvent.cpp  |  8 ++++----
+ tunnel.cpp   |  8 ++++----
+ vdw.cpp      |  8 ++++----
+ volume.cpp   |  8 ++++----
+ 7 files changed, 29 insertions(+), 29 deletions(-)
+
+diff --git a/cavities.cpp b/cavities.cpp
+index 418a1a7..96b6a15 100644
+--- a/cavities.cpp
++++ b/cavities.cpp
+@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 's') {
+@@ -45,11 +45,11 @@ int main(int argc, char *argv[]) {
+     } else if(argv[1][1] == 't') {
+       trim_rad = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+       cerr << "./Cavities.exe -i <file> -g <grid spacing> -s <shell radius> " << endl
+         << "\t-p <probe radius> -t <trim_probe_rad>  " << endl
+diff --git a/channel.cpp b/channel.cpp
+index c5acd20..9040631 100644
+--- a/channel.cpp
++++ b/channel.cpp
+@@ -35,7 +35,7 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'b') {
+       BIGPROBE = atof(&argv[2][0]);
+     } else if(argv[1][1] == 's') {
+@@ -49,13 +49,13 @@ int main(int argc, char *argv[]) {
+     } else if(argv[1][1] == 'z') {
+       z = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+diff --git a/fsv_calc.cpp b/fsv_calc.cpp
+index 9f81347..ef765b8 100644
+--- a/fsv_calc.cpp
++++ b/fsv_calc.cpp
+@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 's') {
+       SMPROBE = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'b') {
+@@ -44,11 +44,11 @@ int main(int argc, char *argv[]) {
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+       cerr << "./FsvCalc.exe -i <file> -b <big_probe> -s <small_probe> " << endl
+         << "\t-t <trim probe> -g <gridspace> " << endl
+diff --git a/solvent.cpp b/solvent.cpp
+index d857696..bc9d67f 100644
+--- a/solvent.cpp
++++ b/solvent.cpp
+@@ -34,7 +34,7 @@ int main(int argc, char *argv[]) {
+  
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);   
++      sprintf(file,"%s",&argv[2][0]);   
+     } else if(argv[1][1] == 's') {
+       SMPROBE = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'b') {
+@@ -42,11 +42,11 @@ int main(int argc, char *argv[]) {
+     } else if(argv[1][1] == 't') {
+       TRIMPROBE = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+diff --git a/tunnel.cpp b/tunnel.cpp
+index 0094d05..7472aaa 100644
+--- a/tunnel.cpp
++++ b/tunnel.cpp
+@@ -40,7 +40,7 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 's') {
+@@ -50,11 +50,11 @@ int main(int argc, char *argv[]) {
+     } else if(argv[1][1] == 't') {
+       trim_prb = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+       cerr << "./Tunnel.exe -i <file> -g <grid spacing> -p <tunnel probe radius>" << endl
+         << "\t-e <EZD outfile> -o <PDB outfile> -m <MRC outfile>" << endl
+diff --git a/vdw.cpp b/vdw.cpp
+index 4df73f5..0e26edc 100644
+--- a/vdw.cpp
++++ b/vdw.cpp
+@@ -32,13 +32,13 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
+diff --git a/volume.cpp b/volume.cpp
+index a2ca9ad..c304b94 100644
+--- a/volume.cpp
++++ b/volume.cpp
+@@ -32,15 +32,15 @@ int main(int argc, char *argv[]) {
+ 
+   while(argc > 1 && argv[1][0] == '-') {
+     if(argv[1][1] == 'i') {
+-      sprintf(file,&argv[2][0]);
++      sprintf(file,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'p') {
+       PROBE = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'o') {
+-      sprintf(pdbfile,&argv[2][0]);
++      sprintf(pdbfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'e') {
+-      sprintf(ezdfile,&argv[2][0]);
++      sprintf(ezdfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'm') {
+-      sprintf(mrcfile,&argv[2][0]);
++      sprintf(mrcfile,"%s",&argv[2][0]);
+     } else if(argv[1][1] == 'g') {
+       GRID = atof(&argv[2][0]);
+     } else if(argv[1][1] == 'h') {
diff --git a/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
new file mode 100644
index 000000000000..556e928d5818
--- /dev/null
+++ b/sci-chemistry/threeV/files/threeV-1.2-gentoo.patch
@@ -0,0 +1,107 @@
+diff --git a/Makefile b/Makefile
+index a58462c..616f51a 100644
+--- a/Makefile
++++ b/Makefile
+@@ -1,7 +1,7 @@
+-CC = g++
+-EXT=$(shell ./cpuflags.pl --opt )
+-FLAGS = -Wall $(EXT)
+-#FLAGS = -O3 -Wall -ffast-math
++CXX ?= g++
++#EXT=$(shell ./cpuCXXFLAGS.pl --opt )
++#CXXFLAGS = -Wall $(EXT)
++#CXXFLAGS = -O3 -Wall -ffast-math
+ OBJS = utils-main.o utils-output.o utils-mrc.o
+ 
+ all:	cav chan fsv sol tun vdw vol
+@@ -17,54 +17,65 @@ volume:	vol
+ objects:	utils-main.o utils-output.o utils-mrc.o
+ 
+ cav:	objects cavities.cpp
+-	$(CC) $(FLAGS) -o Cavities.exe $(OBJS) cavities.cpp
+-	chmod 777 Cavities.exe
+-	mv Cavities.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o cavities.o cavities.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Cavities $(OBJS) cavities.o
++	chmod 755 Cavities
++	mv Cavities ../bin
+ 
+ chan:	objects channel.cpp
+-	$(CC) $(FLAGS) -o Channel.exe $(OBJS) channel.cpp
+-	chmod 777 Channel.exe
+-	mv Channel.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o channel.o channel.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Channel $(OBJS) channel.o
++	chmod 755 Channel
++	mv Channel ../bin
+ 
+ fsv:	objects fsv_calc.cpp
+-	$(CC) $(FLAGS) -o FsvCalc.exe $(OBJS) fsv_calc.cpp
+-	chmod 777 FsvCalc.exe
+-	mv FsvCalc.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o fsv_calc.o fsv_calc.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o FsvCalc $(OBJS) fsv_calc.o
++	chmod 755 FsvCalc
++	mv FsvCalc ../bin
+ 
+ sol:	objects solvent.cpp
+-	$(CC) $(FLAGS) -o Solvent.exe $(OBJS) solvent.cpp
+-	chmod 777 Solvent.exe
+-	mv Solvent.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o solvent.o solvent.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Solvent $(OBJS) solvent.o
++	chmod 755 Solvent
++	mv Solvent ../bin
+ 
+ tun:	objects tunnel.cpp
+-	$(CC) $(FLAGS) -o Tunnel.exe $(OBJS) tunnel.cpp
+-	chmod 777 Tunnel.exe
+-	mv Tunnel.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o tunnel.o tunnel.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Tunnel $(OBJS) tunnel.o
++	chmod 755 Tunnel
++	mv Tunnel ../bin
+ 
+ vdw:	objects vdw.cpp
+-	$(CC) $(FLAGS) -o VDW.exe $(OBJS) vdw.cpp
+-	chmod 777 VDW.exe
+-	mv VDW.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o vdw.o vdw.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o VDW $(OBJS) vdw.o
++	chmod 755 VDW
++	mv VDW ../bin
+ 
+ vol:	objects volume.cpp
+-	$(CC) $(FLAGS) -o Volume.exe $(OBJS) volume.cpp
+-	chmod 777 Volume.exe
+-	mv Volume.exe ../bin
++	$(CXX) $(CXXFLAGS) -c -o volume.o volume.cpp
++	$(CXX) $(CXXFLAGS) $(LDFLAGS) -o Volume $(OBJS) volume.o
++	chmod 755 Volume
++	mv Volume ../bin
+ 
+ utils-main.o:	utils-main.cpp
+-	$(CC) $(FLAGS) -c -o utils-main.o utils-main.cpp
++	$(CXX) $(CXXFLAGS) -c -o utils-main.o utils-main.cpp
+ 
+ utils-output.o:	utils-main.o utils-output.cpp
+-	$(CC) $(FLAGS) -c -o utils-output.o utils-output.cpp
++	$(CXX) $(CXXFLAGS) -c -o utils-output.o utils-output.cpp
+ 
+ utils-mrc.o:	utils-mrc.cpp
+-	$(CC) $(FLAGS) -c -o utils-mrc.o utils-mrc.cpp
++	$(CXX) $(CXXFLAGS) -c -o utils-mrc.o utils-mrc.cpp
++
++install:
++	install -d $(DESTDIR)/usr/bin
++	install ../bin/* $(DESTDIR)/usr/bin/
+ 
+ clean:
+ 	rm -fv *.o  *~
+ 
+ distclean:
+-	rm -fv *.o ../bin/*.exe *~
++	rm -fv *.o ../bin/* *~
+ 
+ none:	
+ 	echo "Please type make xxx, where xxx = cav, cha, fsv, sol, tun, vdw, or vol"
diff --git a/sci-chemistry/threeV/metadata.xml b/sci-chemistry/threeV/metadata.xml
new file mode 100644
index 000000000000..da36ecbfcd6a
--- /dev/null
+++ b/sci-chemistry/threeV/metadata.xml
@@ -0,0 +1,8 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE pkgmetadata SYSTEM "http://www.gentoo.org/dtd/metadata.dtd">
+<pkgmetadata>
+	<maintainer type="project">
+		<email>sci-chemistry@gentoo.org</email>
+		<name>Gentoo Chemistry Project</name>
+	</maintainer>
+</pkgmetadata>
diff --git a/sci-chemistry/threeV/threeV-1.2-r1.ebuild b/sci-chemistry/threeV/threeV-1.2-r1.ebuild
new file mode 100644
index 000000000000..1d4a1e1f3466
--- /dev/null
+++ b/sci-chemistry/threeV/threeV-1.2-r1.ebuild
@@ -0,0 +1,40 @@
+# Copyright 1999-2017 Gentoo Foundation
+# Distributed under the terms of the GNU General Public License v2
+
+EAPI=6
+
+inherit toolchain-funcs
+
+DESCRIPTION="3V: Voss Volume Voxelator"
+HOMEPAGE="http://geometry.molmovdb.org/3v/"
+SRC_URI="http://geometry.molmovdb.org/3v/3v-${PV}.tgz"
+
+LICENSE="GPL-2"
+SLOT="0"
+KEYWORDS="~amd64 ~x86 ~amd64-linux ~x86-linux"
+IUSE=""
+
+PDEPEND="sci-chemistry/msms-bin"
+#	sci-chemistry/usf-rave"
+
+S="${WORKDIR}/3v-${PV}/src"
+
+PATCHES=(
+	"${FILESDIR}"/${P}-gentoo.patch
+	"${FILESDIR}"/${P}-format-security.patch
+)
+
+src_prepare() {
+	default
+	tc-export CXX
+	emake distclean
+
+	export MAKEOPTS+=" V=1"
+}
+
+src_install() {
+	emake DESTDIR="${ED}" install
+
+	cd .. || die
+	dodoc AUTHORS ChangeLog QUICKSTART README TODO VERSION
+}